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JTreeview is a handy, easy to use tool designed to help you view tree files. This viewer is limited to Newick format (or the custom save format, based on Newick). Trees can be viewed as either rooted or unrooted, rerooted and every node and leaf node names can be highlighted using regular expression searches (red dot in rooted tree).
One interesting feature is the ability to load a sequence alignment containing the sequences present in the tree. This allows the user to select a subtree (branch) and examine the alignment of the sequences present in only that branch.
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